Contacts of the helix formed by residues 63 - 76 (chain C) in PDB entry 3QB4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 63 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PRO* 6.2 0.2 - - - +
90A LEU* 4.9 11.4 - - + +
111A ASP* 3.9 29.6 - - + +
61C GLU 3.5 0.6 + - - -
62C PRO* 1.3 77.1 - - - +
64C ASN* 1.3 65.6 + - - +
65C HIS* 3.5 7.6 + - - +
66C ALA* 3.0 25.7 + - - +
67C VAL* 3.1 20.1 + - - +
120C ARG* 4.0 28.3 + - - +
81D GLU* 5.2 3.4 - - - -
82D GLY* 5.4 0.4 - - - -
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Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.9 20.2 - - - +
110A GLU 2.7 37.2 + - - +
111A ASP* 3.7 1.0 + - - +
112A MET* 3.6 15.9 - - - -
62C PRO 4.1 0.4 + - - -
63C THR* 1.3 71.7 - - - +
65C HIS* 1.3 64.0 + - - +
67C VAL* 3.1 9.6 + - - +
68C ILE* 3.0 27.3 + - - +
81D GLU* 3.4 27.7 + - - +
82D GLY* 3.5 25.0 + - - -
85D PHE* 3.7 13.7 - - + -
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Residues in contact with HIS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.4 2.1 - - + +
43A TYR* 5.6 0.2 - - - -
45A ALA* 3.1 18.2 + - + +
46A PHE 2.6 30.3 + - - -
47A HIS* 4.4 1.8 - - - -
87A PRO* 4.4 10.2 - - + +
90A LEU* 3.7 15.9 - - + -
111A ASP 2.7 23.9 + - - +
112A MET* 3.1 26.7 - - - +
114A VAL* 3.5 16.3 - - + +
63C THR* 3.1 3.9 - - - +
64C ASN* 1.3 73.6 - - - +
66C ALA* 1.3 59.5 + - - +
68C ILE* 3.3 7.6 + - + +
69C GLN* 2.9 52.9 + - + +
120C ARG* 4.7 1.6 + - - -
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 4.4 3.1 - - + -
62C PRO* 4.1 4.9 - - + -
63C THR* 3.0 24.4 + - - +
65C HIS* 1.3 74.4 + - - +
67C VAL* 1.3 61.7 + - - +
70C THR* 2.8 35.4 + - - -
83C THR* 3.6 16.5 - - + +
119C CYS 3.7 23.1 - - - +
120C ARG* 3.8 13.9 - - - +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 5.5 0.9 - - + -
56C LEU* 4.4 3.1 - - + -
62C PRO* 3.6 24.7 - - + -
63C THR 3.1 15.4 + - - +
64C ASN* 3.5 9.6 - - - +
66C ALA* 1.3 77.8 - - - +
68C ILE* 1.3 57.2 + - - +
70C THR* 3.3 5.6 + - - -
71C LEU* 2.9 36.4 + - + +
82D GLY* 4.1 13.0 - - - +
85D PHE* 3.6 26.0 - - + -
86D GLN* 3.5 37.2 - - + +
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 5.8 1.3 - - + -
26A VAL* 3.7 33.4 - - + -
28A PHE* 5.3 3.6 - - + -
31A MET* 4.3 6.1 - - + -
33A TRP* 4.0 25.6 - - + -
43A TYR* 3.9 16.8 - - - +
45A ALA* 5.5 2.5 - - + -
112A MET* 4.6 2.5 - - + -
64C ASN 3.0 16.1 + - - +
65C HIS* 3.6 9.0 - - + +
67C VAL* 1.3 72.2 - - - +
69C GLN* 1.3 55.8 + - - +
71C LEU* 3.2 6.3 + - + +
72C MET* 2.8 41.5 + - + +
85D PHE* 3.7 33.2 - - + -
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.4 8.0 - - + +
47A HIS* 3.6 20.6 + - - +
48A CYS 5.1 3.1 + - - -
65C HIS* 2.9 43.3 + - + +
68C ILE* 1.3 73.5 - - - +
70C THR* 1.3 52.1 + - - +
72C MET* 3.1 6.5 + - - +
73C ASN* 2.7 34.5 + - - +
80C THR* 3.6 10.8 - - + -
81C PRO* 2.9 36.4 + - - +
82C PRO 3.3 15.4 + - - -
83C THR* 3.9 19.6 - - + +
120C ARG* 5.2 1.9 - - - +
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C CYS 4.4 6.3 + - - +
53C GLU* 4.2 4.0 - - - -
54C PHE* 3.6 41.3 - - + +
56C LEU* 3.5 21.1 - - + +
66C ALA 2.8 26.6 + - - -
67C VAL* 3.6 5.4 - - - -
69C GLN* 1.3 73.4 - - - +
71C LEU* 1.3 64.7 + - - +
73C ASN* 3.3 8.6 + - + +
74C SER* 3.0 22.1 + - - -
82C PRO* 5.9 0.4 - - - -
83C THR* 3.6 17.7 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 3.9 11.9 - - + -
33A TRP* 3.7 37.2 - - + -
54C PHE* 3.7 26.9 - - + -
67C VAL* 2.9 28.9 + - + +
68C ILE* 3.4 8.1 - - - +
70C THR* 1.3 75.6 - - - +
72C MET* 1.3 58.4 + - - +
74C SER* 3.1 6.7 + - - +
75C MET* 3.0 31.9 + - - +
85D PHE* 4.1 9.4 - - + +
89D ASP* 3.5 25.4 - - - +
90D SER* 4.0 12.2 - - - +
97D ARG* 4.0 5.8 - - - +
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Residues in contact with MET 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.9 19.3 - - + -
25A HIS 3.6 20.9 - - - +
26A VAL* 3.8 31.2 - - - -
27A ASN 5.5 1.1 - - - +
31A MET* 4.5 11.4 - - + +
68C ILE* 2.8 26.7 + - - +
69C GLN 3.7 3.4 - - - +
71C LEU* 1.3 69.7 - - - +
73C ASN* 1.3 65.5 + - - +
75C MET* 3.2 27.5 + - + +
76C ASP* 3.1 23.4 + - - +
79C SER* 5.7 2.7 - - - +
80C THR* 3.7 25.2 + - + +
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLN 2.7 20.4 + - - +
70C THR* 3.6 7.6 - - + +
72C MET* 1.3 74.3 - - - +
74C SER* 1.3 59.8 + - - +
76C ASP 4.4 0.4 - - - -
77C PRO* 3.0 41.3 + - - +
80C THR* 2.5 31.8 + - - +
81C PRO* 3.2 8.2 - - - +
82C PRO* 3.2 36.6 - - + +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 4.9 6.7 - - - +
70C THR* 3.0 13.2 + - - -
71C LEU* 3.1 11.9 + - - +
73C ASN* 1.3 79.2 - - - +
75C MET* 1.3 54.4 + - - +
77C PRO* 4.7 1.1 - - - -
90D SER* 6.0 0.5 - - - -
93D ALA* 4.1 4.3 - - - +
94D GLN* 2.8 39.3 + - - +
95D LEU* 4.7 2.2 + - - -
97D ARG* 3.3 35.5 + - - -
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Residues in contact with MET 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.5 32.5 - - + +
31A MET* 3.7 31.9 - - + -
71C LEU 3.0 20.0 + - - +
72C MET* 3.5 24.0 - - + +
74C SER* 1.3 78.1 - - - +
76C ASP* 1.3 63.4 + - + +
90D SER* 4.0 11.7 - - - +
92D LYS* 3.8 33.9 - - + +
93D ALA* 4.2 1.3 - - - +
94D GLN* 2.9 16.5 - - - +
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Residues in contact with ASP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET 3.1 10.4 + - - +
73C ASN 3.5 2.2 - - - -
75C MET* 1.3 85.3 - - + +
77C PRO* 1.3 63.3 - - - +
78C GLU* 2.9 28.4 + - - +
79C SER* 2.9 38.5 + - - +
80C THR* 3.1 10.9 + - - +
94D GLN* 4.1 1.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il